NetworCh Documentation
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NetworCh manuals: Getting started
NetworCh: Documentation
Nicolas Bertin
October 2016
This page contains a non-exhaustive list of the main Matlab functions available in the NetworCh library.
Common functions
| Utility functions | |
|---|---|
| all_segments_length.m | Return the lengths of all segments by applying PBC |
| find_segment.m | Find the position of a given segment within the links list |
| generate_connectivity.m | Generate nodal connectivity table corresponding to the links list |
| pbc_fold.m | Folds point(s) into the primary volume by applying PBC |
| pbc_position.m | Returns the closest image of a point to another by applying PBC |
| segment_length.m | Compute length of a given segment by applying PBC |
| test_structure.m | Generate test structures to test network functions |
| Network manipulation | |
| chop_structure.m | Extract a slice of the network by chopping the structure in a selected direction |
| extract_links.m | Extract a sub-network that only contains given links from the original network |
| extract_nodes.m | Extract a sub-network that only contains given nodes from the original network |
| remove_double_links.m | Remove double-links from the network |
| remove_link.m | Remove a given link from the network |
| remove_nodes.m | Remove given nodes from the network |
| remove_self_loops.m | Remove self-loops from the network |
| replicate_volume.m | Duplicate initial network by assembling 2 periodic replica in a given direction |
| replicate_volume_3.m | Replicate initial network by assembling 3 periodic replica in a given direction |
| scale_structure.m | Rescale a structure by a scaling factor |
| Geometrical functions | |
| facet_intersection.m | Find which facet of the rectangular primary volume is intersected by a given segment |
| facet_intersection_position.m | Determine the facet and the intersection point between the rectangular primary volume and a given segment |
| find_box_neighbors.m | Find neighbors of a given node based on box partitioning |
| outside_box.m | Check if point(s) lie(s) outside of the primary volume |
| partition_box.m | Sort nodes by partitioning the primary volume into boxes |
| segment_plane_intersection.m | Compute the intersection between a plane and a given segment |
| Visualization functions | |
| plot_box.m | Plot the box delimiting the primary volume |
| plot_nodes.m | Plot a subset of nodes of the network |
| plot_segments.m | Plot a subset of segments of the network |
| plot_structure.m | Plot the full network structure |
| Export functions | |
| export_gexf.m | Export the network in GEXF format |
| export_gml.m | Export the network in GML format |
Functions for DD structures analysis
| Utility functions | |
|---|---|
| fcc_slip_system.m | Get Burgers vector and slip plane normal for a given FCC slip system |
| get_slip_system.m | Determine the slip system of segment with a given Burgers vector b and slip plane normal |
| is_junction_segment.m | Determine if a given segment (or list of segments) corresponds to a dislocation junction |
| structure_sanity_check.m | Perform several sanity checks on the DD structure (conservation of the Burgers vector, zero-arm nodes, self-loops, double-links, ...) |
| unique_slip_plane.m | Determine properties of the unique slip plane of a given segment (including the intercept coefficient) |
| Structure generation | |
| generate_fcc_junction.m | Generate the initial configuration (two straight segments connected at their middle point) to form a FCC junction (Lomer, glissile, Hirth or colinear) at given angles |
| generate_frs.m | Generate a straight Frank-Read source in a periodic cubic volume |
| generate_glissile_loop.m | Generate a glissile dislocation loop |
| generate_infinite_line.m | Generate an infinite dislocation line in a periodic cubic volume |
| generate_prismatic_loop.m | Generate a prismatic dislocation loop (4 nodes) |
| Structure decomposition | |
| decompose_into_loops.m | Decompose the dislocation network into loops by unzipping binary junctions |
| irreductible_structure.m | Fully decompose the DD structure into an irredducible core by recursively unzipping junctions and reducing the network (removing self-links, merging double-links, ...) |
| merge_double_links.m | Merge double-links of the DD network |
| physical_structure.m | Reduce the DD structure to physical nodes only by removing all discretization nodes |
| reduce_structure.m | Fully reduce the DD structure by recursively removing the self and double links, and the discretization nodes |
| Import / Export structures | |
| read_data_files.m | List all ParaDiS data files in a given directory |
| read_dxa_file.m | Read dislocations from a DXA (Ovito) .ca file |
| read_nodes.m | Read dislocation nodes from a ParaDiS data file |
| write_data_file.m | Write DD structure into a ParaDiS nodal data file |
Functions for MD structures analysis
| read_cgsd.m | Read CGSD files (.cn and .bnd) |
| merge_cross_links.m | Merge cross-linked nodes into single nodes and flag them |
Functions for network analysis
| adjacency.m | Generate the adjacency matrix from the links/segments list |
| assortativity.m | Calculate the Pearson correlation coefficient that measures the assortativity of the nodes of the network |
| average_degree.m | Calculate the average nodes degree and the exponent of best fit power-law distribution |
| average_shortest_path.m | Compute the average shortest path between all pairs of nodes of the network |
| clustering.m | Calculate the clustering and transitivity coefficients of the network |
| construct_shortest_path.m | Construct the shortest path (sequence of nodes) from a source to a target node |
| extract_component.m | Extract a given component from the network |
| find_components.m | Find unconnected components of the network |
| link_density.m | Calculate the link density of the network |
| normalized_laplacian.m | Compute the normalized graph Laplacian matrix of the network |
| random_network.m | Generate a random network that follows a power-law degree distribution |
| shortest_path.m | Compute shortest path from a source to all other vertices or to a given target |